New paper template

Author 11,2,* , Author 21,2, Author 33, Author 4E4
1Heidelberg University, Centre for Organismal Studies (COS), 69120 Heidelberg, Germany
2Affiliation 2
3Affiliation 3
4Affiliation 4
*Correspondence: xy@cos.uni-heidelberg.de

Abstract

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

dit is echt zo veel beter vette shit[Oh et al. (2014)](Gelderen et al. 2017; Hayes et al. 2019; Gelderen and Pierik 2020; García-González and Gelderen 2021; Gelderen 2021)(Gelderen et al. 2018)

text in bold italic underline

Introduction

You can add references either by referring to their id in the .bib file e.g., (Marinković et al. 2019), or by switching to the visual editor (Cogwheel in the .Rmd menu -> Use Visual Editor). [Jokura et al. (2023)](Jokura et al. 2023)(Jacobs and Ryu 2023)

It is now a test to edit the text and see how the changes show up on GitHub.

Test of git show.

In the visual editor mode, go to ‘Insert’ -> @ Citation

You can select a Zotero library, PubMed, CrossRef etc. and insert the citations. (Jacobs and Ryu 2023)

The easiest way is to use the command line:

curl -LH "Accept: application/x-bibtex" https://doi.org/10.7554/eLife.91258.1 >> references.bib

Platynereis dumerilii is a marine annelid… (Ozpolat et al. 2021)

The references are stored in manuscript/references.bib (need to be defined in the Yaml header). This file will automatically updated when you insert a new reference through the Visual editor > Insert > Citations.

In this documents, references will be formatted in the style of eLife. This is defined in the Yaml header under: csl: elife.csl. The elife.csl file is saved in the /manuscript folder.

If you would like to use a different citation format, download the respective .csl file (e.g., from the Zotero style repository https://www.zotero.org/styles), save it in the /manuscript folder of the project and change the Yaml to csl: your_favourite_journal.csl.

Results

Inserting Figures

Test comment here.

You can add your figures into the rendered document. We saved the figures into /manuscript/figures or /manuscript/figure_supplements and can insert them from there. We use knitr::include_graphics for this. The title and legend can also be edited, as will as the width of the output figure. Test comment behaviour:

Figure 1. A figure (A) A nice picture of whatever. (B) legend. (C)
(D)

Figure 1. Our nice figure from yesterday (A) A nice picture. (B) legend. (C)
(D)

Figure 3. Fianlly some ril data (A) A nice picture. (B) legend. (C)
(D)

Equations

Equations can also be inserted, Insert -> Display Math:

\[ \bar{X} = \frac{\sum_{i=1}^{n} x_{i}}{n} \]


Sourcing code and working with variable

The mean value of Nanog expression was 0.0909 indicating that Nanog is downregulated. The ‘analysis/scripts/statistics_for_paper.R’ script is sourced and it runs but the output is not included in the knitted output. But we can access the variables defined in the sourced script simply by adding ` r var_name ` between ` backticks, in this case max_PRC value is 21 (now this number comes from our sourced script).

If we update the data, the script can recalculate the variable we want to refer to in the text and update the number.

Acknowledgements

We would like to thank the Jekely lab for the R project template (https://github.com/JekelyLab/new_paper_template) we used to write this paper. This work was funded by …

Materials and Methods

You can insert tables from source data, such as .csv or Excel files and render them in html with the tinytable package.

Alternatively, you can use the Markdown grid table format. For more complex tables, you can use the tablesgenerator online grid table editor/converter (e.g. converts csv or excel files).

The output may differ between html and pdf, for most consistent results use the grid table format described here.

Key Resources Table

tinytable_kqfr4owusvectetg2u4g
Reagent type (species) or resource Designation Source or reference Identifiers Additional information
biological sample (N. vectensis) larval, juvenile and adult N. vectensis Specimens obtained form the Marine Invertebrate Culture Unit of the University of Exeter N/A NA
biological sample (cDNA) cDNA obtained from N. vectensis this study N/A RNA extracted with Trizol and cDNA synthesized with cDNA synthesis kit according to manufacturers recommendation
biological sample (peptide extract) peptide extracts obtained from N. vectensis this study N/A Peptides extracted from N. vectensis according to protocol explained in Material and Methods
genetic reagent (cDNA synthesis) SuperScript™ III First-Strand Synthesis System Invitrogen (from ThermoFisher) 18080051 NA
genetic reagent (Polymerase) Q5® Hot Start High-Fidelity DNA Polymerase  New England Biolabs M0493L NA
genetic reagent (DNA assembly) NEBuilder® HiFi DNA Assembly Master Mix New England Biolabs E2621L NA
genetic reagent (restriction enzyme) EcoRV restriction enzyme New England Biolabs R3195L NA
genetic reagent (restriction enzyme) Afl2 restriction enzyme New England Biolabs R0520L NA
tinytable_g2nr7pltst2c9vmfe9ue
length genotype treatment
0.9245671 Col-0 WL
1.0218615 Col-0 WL
0.9966017 Col-0 WL
0.9505628 Col-0 WL
0.9268615 Col-0 WL
1.0157576 Col-0 WL
0.8461255 Col-0 WL
1.1062338 Col-0 WL
0.9379654 Col-0 WL
1.0031385 Col-0 WL
1.0631007 Col-0 WL
1.0244245 Col-0 WL
1.0452950 Col-0 WL
0.9827914 Col-0 WL
1.1515468 Col-0 WL
1.0773453 Col-0 WL
0.9130360 Col-0 WL
0.8041727 Col-0 WL
0.9983525 Col-0 WL
1.1918849 Col-0 WL
1.6545634 Col-0 WL+FR
1.8239328 Col-0 WL+FR
1.6717808 Col-0 WL+FR
1.7176938 Col-0 WL+FR
1.6410200 Col-0 WL+FR
2.1711498 Col-0 WL+FR
2.0464760 Col-0 WL+FR
2.0167587 Col-0 WL+FR
1.6328243 Col-0 WL+FR
2.3739322 Col-0 WL+FR
2.0800776 Col-0 WL+FR
1.6138511 Col-0 WL+FR
1.7080964 Col-0 WL+FR
1.3430332 Col-0 WL+FR
1.7769754 Col-0 WL+FR
1.7099929 Col-0 WL+FR
1.4771922 Col-0 WL+FR
2.1760686 Col-0 WL+FR
1.8223416 Col-0 WL+FR
1.8091305 Col-0 WL+FR
1.4077800 bbx202122 WL
1.5467519 bbx202122 WL
1.5741903 bbx202122 WL
1.4299217 bbx202122 WL
1.1990833 bbx202122 WL
1.2584101 bbx202122 WL
1.6343420 bbx202122 WL
1.4866870 bbx202122 WL
1.5373525 bbx202122 WL
1.1469634 bbx202122 WL
1.6091541 bbx202122 WL
1.3436566 bbx202122 WL
1.6311238 bbx202122 WL
1.6916648 bbx202122 WL
1.7468812 bbx202122 WL
1.5090676 bbx202122 WL
1.4163621 bbx202122 WL
1.7467081 bbx202122 WL
3.3603373 bbx202122 WL+FR
2.8432512 bbx202122 WL+FR
2.4912563 bbx202122 WL+FR
2.1789593 bbx202122 WL+FR
2.8216115 bbx202122 WL+FR
2.6474588 bbx202122 WL+FR
3.1705275 bbx202122 WL+FR
3.0144364 bbx202122 WL+FR
3.1252673 bbx202122 WL+FR
4.1394364 bbx202122 WL+FR
3.7884321 bbx202122 WL+FR
2.3440535 bbx202122 WL+FR
3.4638728 bbx202122 WL+FR
3.4085116 bbx202122 WL+FR
2.7177095 bbx202122 WL+FR
2.1718353 bbx202122 WL+FR
1.0043299 BBX20ox11d WL
0.9370565 BBX20ox11d WL
0.7852869 BBX20ox11d WL
0.8078840 BBX20ox11d WL
1.1030492 BBX20ox11d WL
0.8559703 BBX20ox11d WL
0.8926352 BBX20ox11d WL
0.9839805 BBX20ox11d WL
1.2239153 BBX20ox11d WL
0.8539270 BBX20ox11d WL
0.9747448 BBX20ox11d WL
1.1971124 BBX20ox11d WL
1.0977369 BBX20ox11d WL
1.0473818 BBX20ox11d WL
1.2541844 BBX20ox11d WL
1.3249771 BBX20ox11d WL+FR
1.5655777 BBX20ox11d WL+FR
1.3409857 BBX20ox11d WL+FR
1.6575733 BBX20ox11d WL+FR
1.2952776 BBX20ox11d WL+FR
1.8147405 BBX20ox11d WL+FR
1.9365644 BBX20ox11d WL+FR
1.8706203 BBX20ox11d WL+FR
2.6305337 BBX20ox11d WL+FR
1.7576376 BBX20ox11d WL+FR
2.2232545 BBX20ox11d WL+FR
2.2839026 BBX20ox11d WL+FR
2.0044802 BBX20ox11d WL+FR
1.9484573 BBX20ox11d WL+FR
1.3261761 BBX20ox11d WL+FR
Grid Table example
Col1 Col2 Col3 Col4 Col5
a b c d e
d
STUPIDTABLE
Col1 Col2 Col3
1 2 3
325 235 4
532 X X

Complex grid table example

This table was generated by tt() as the output of an r chunk in a Quarto doc. For larger multi-page tables, this method gives correct page breaks in the pdf and html outputs. You can change the relative column widths with {tbl-colwidths=“[10,20,20,20,30]”} placed after the table caption declaration at the end.

More complex Grid Table example
Reagent type (species) or resource Designation Source or reference Identifiers Additional information
biological sample (N. vectensis) larval, juvenile and adult N. vectensis Specimens obtained form the Marine Invertebrate Culture Unit of the University of Exeter N/A NA
biological sample (cDNA) cDNA obtained from N. vectensis this study N/A RNA extracted with Trizol and cDNA synthesized with cDNA synthesis kit according to manufacturers recommendation
biological sample (peptide extract) peptide extracts obtained from N. vectensis this study N/A Peptides extracted from N. vectensis according to protocol explained in Material and Methods
genetic reagent (cDNA synthesis) SuperScript™ III First-Strand Synthesis System Invitrogen (from ThermoFisher) 18080051 NA
genetic reagent (Polymerase) Q5® Hot Start High-Fidelity DNA Polymerase New England Biolabs M0493L NA
genetic reagent (DNA assembly) NEBuilder® HiFi DNA Assembly Master Mix New England Biolabs E2621L NA
genetic reagent (restriction enzyme) EcoRV restriction enzyme New England Biolabs R3195L NA
genetic reagent (restriction enzyme) Afl2 restriction enzyme New England Biolabs R0520L NA

References

References

García-González J and Gelderen K van. Bundling up the role of the actin cytoskeleton in primary root growth. Frontiers in Plant Science. 2021:12. https://doi.org/10.3389/fpls.2021.777119
Gelderen K van. Can I have some light and sugar with my nitrate? Plant Physiology. 2021:186(1):196–197. https://doi.org/10.1093/plphys/kiab068
Gelderen K van, Kang C, Paalman R, Keuskamp D, Hayes S, and Pierik R. Far-Red Light Detection in the Shoot Regulates Lateral Root Development through the HY5 Transcription Factor. The Plant Cell. 2018:30(1):101–116. https://doi.org/10.1105/tpc.17.00771
Gelderen K van, Kang C, and Pierik R. Light Signaling, Root Development, and Plasticity. Plant Physiology. 2017:176(2):1049–1060. https://doi.org/10.1104/pp.17.01079
Gelderen K van and Pierik R. Warm days, relaxed RNA. Nature Plants. 2020:6(5):438–439. https://doi.org/10.1038/s41477-020-0643-1
Hayes S, Pantazopoulou CK, Gelderen K van, Reinen E, Tween AL, Sharma A, Vries M de, Prat S, Schuurink RC, Testerink C, et al. Soil Salinity Limits Plant Shade Avoidance. Current Biology. 2019:29(10):1669–1676.e4. https://doi.org/10.1016/j.cub.2019.03.042
Jacobs EAK and Ryu S. Larval zebrafish as a model for studying individual variability in translational neuroscience research. Frontiers in Behavioral Neuroscience. 2023:17. https://doi.org/10.3389/fnbeh.2023.1143391
Jokura K, Ueda N, Gühmann M, Yañez-Guerra LA, Słowiński P, Wedgwood KCA, and Jékely G. Nitric oxide feedback to ciliary photoreceptor cells gates a UV avoidance circuit. 2023. https://doi.org/10.7554/elife.91258.1
Marinković M, Berger J, and Jékely G. Neuronal coordination of motile cilia in locomotion and feeding. Philosophical Transactions of the Royal Society B: Biological Sciences. 2019:375(1792):20190165. https://doi.org/10.1098/rstb.2019.0165
Oh E, Zhu J-Y, Bai M-Y, Arenhart RA, Sun Y, and Wang Z-Y. Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl. eLife. 2014:3:e03031. https://doi.org/10.7554/eLife.03031
Ozpolat BD, Randel N, Williams EA, Bezares-Calderón LA, Andreatta G, Balavoine G, Bertucci PY, Ferrier DEK, Gambi MC, Gazave E, et al. The Nereid on the rise: Platynereis as a model system. Zenodo. 2021. https://doi.org/10.5281/ZENODO.4907400